<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/13226?offset=1000</link>
	<atom:link href="https://bioinformaticsonline.com/related/13226?offset=1000" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly</guid>
	<pubDate>Mon, 24 Jul 2023 07:04:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly</link>
	<title><![CDATA[Bioinformatics tools for genome assembly !]]></title>
	<description><![CDATA[<p>There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:</p><ol>
<li>
<p><span>SPAdes:</span> An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.</p>
</li>
<li>
<p><span>ABySS:</span> A parallelized assembler for large genomes that uses de Bruijn graphs.</p>
</li>
<li>
<p><span>Velvet:</span> Another de Bruijn graph-based assembler optimized for short-read sequencing data.</p>
</li>
<li>
<p><span>SOAPdenovo:</span> A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.</p>
</li>
<li>
<p><span>MaSuRCA:</span> A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.</p>
</li>
<li>
<p><span>Canu:</span> A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.</p>
</li>
<li>
<p><span>Flye:</span> A long-read assembler suitable for bacterial and small eukaryotic genomes.</p>
</li>
<li>
<p><span>SMARTdenovo:</span> An assembler designed for long reads, particularly suited for PacBio data.</p>
</li>
<li>
<p><span>SPAdes Long Read (SPAdesLR):</span> An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.</p>
</li>
<li>
<p><span>Minia:</span> An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.</p>
</li>
<li>
<p><span>Unicycler:</span> A hybrid assembler that combines short and long reads for circular bacterial genome assembly.</p>
</li>
<li>
<p><span>wtdbg2:</span> A de Bruijn graph assembler for long reads, efficient for very large genomes.</p>
</li>
<li>
<p><span>Shasta:</span> A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.</p>
</li>
<li>
<p><span>Sparc:</span> An assembler designed to handle noisy long reads from Nanopore sequencing.</p>
</li>
<li>
<p><span>CANA:</span> An assembler for metagenomic data, particularly for complex and diverse microbial communities.</p>
</li>
<li>
<p><span>Ra</span> Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.</p>
</li>
</ol><p>Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</guid>
	<pubDate>Mon, 24 Nov 2025 05:16:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</link>
	<title><![CDATA[Bioinformatics: The Bridge Between Curiosity and Discovery]]></title>
	<description><![CDATA[<p>In the sprawling universe of modern science, bioinformatics stands as one of the most transformative and empowering fields of our time. It is where biology meets computation, where data becomes meaning, and where curiosity becomes discovery. If you&rsquo;ve stepped into this world&mdash;or are considering it&mdash;here&rsquo;s your reminder: you&rsquo;re part of a revolution.</p><p><strong>Why Bioinformatics Matters More Than Ever</strong></p><p>Every day, our world generates massive amounts of biological data&mdash;from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.</p><p>Bioinformatics isn&rsquo;t just a skill.<br />It&rsquo;s the language of the future of biology.</p><p>By mastering it, you give yourself the power to:</p><p>Decode genomes and understand life at its most fundamental level</p><p>Identify patterns no microscope could ever reveal</p><p>Predict disease outbreaks before they occur</p><p>Accelerate drug discovery with computational precision</p><p>Contribute to open-source tools that empower scientists worldwide</p><p>You don&rsquo;t just follow science&mdash;you drive it.</p><p><strong>Every Expert Was Once a Beginner</strong></p><p>Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.</p><p>But here&rsquo;s the truth: every bioinformatician started exactly where you are now&mdash;curious, unsure, but excited.</p><p>No one writes perfect code on day one.</p><p>No one understands genomics pipelines immediately.</p><p>What makes you a bioinformatician is not perfection, but perseverance.</p><p>When your script throws a cryptic error&hellip;<br />When your data refuses to format&hellip;<br />When your pipeline runs for 6 hours only to crash&hellip;</p><p>Remember: this is part of the journey.<br />Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.</p><p>Bioinformatics Is Not Just a Career&mdash;It&rsquo;s a Mindset</p><p>It&rsquo;s the mindset of:</p><p>Problem-solving.</p><p>Continuous learning.</p><p>Turning chaos into clarity.</p><p>Seeing what others can&rsquo;t.</p><p>Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.</p><p><strong>Your Contribution Matters</strong></p><p>As you work on your script, pipeline, genome, or model, remember:</p><p>Somewhere, your analysis might contribute to:</p><p>A new therapy</p><p>A faster diagnostic test</p><p>A better understanding of a pathogen</p><p>A more resilient crop</p><p>An open-source dataset that helps thousands</p><p>A discovery that rewrites textbooks</p><p>Your code may be small, but its ripple effect is powerful.</p><p>The Future Is Bioinformatics&mdash;And You Are Part of It</p><p>The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.</p><p>This is a golden era&mdash;and you are not late.<br />You are exactly where you need to be.</p><p>Keep Pushing. Keep Learning. Keep Discovering.</p><p>Bioinformatics is a journey filled with challenges, but also with unmatched rewards.</p><p>So the next time you feel stuck, frustrated, or overwhelmed, remember:<br />You&rsquo;re building the science of tomorrow.</p><p>Be proud. Stay curious. Keep going.<br />Your work matters more than you think.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4946/crcri-bioinfomatics-walk-in-on-08102013</guid>
  <pubDate>Fri, 27 Sep 2013 10:59:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[CRCRI Bioinfomatics Walk In on 08.10.2013]]></title>
  <description><![CDATA[
<p>Walk-in-Interview for recruitment of one Project Fellow for a period of 10 months purely on temporary basis is proposed to be held at Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram for a KSCSTE funded project entitled “PARTICIPATORY DEVELOPMENT OF A WEB BASED USER FRIENDLY CASSAVA EXPERT SYSTEM”</p>

<p>Salary: Rs. 10,000/- per month.</p>

<p>Age limit: 35 for men and 40 for women &amp; SC/ST.</p>

<p>Qualification: First class in M. Sc (Agriculture)/MCA/M.Sc (IT)/ M. Sc (Computer Application)/M.Sc (Bioinformatics)/M.Sc (Geoinformatics).</p>

<p>Desirable: Two years experience in web design and web programming.</p>

<p>Date &amp; time of interview: 08.10.2013, 10 am</p>

<p>Interested candidates may appear for an interview at this institute along with their application in plain paper containing the following particulars viz. (1) Name (2) Father/Husband/Guardian’s Name (3) date of birth &amp; age as on 01.10.2013 (4) Permanent address (5) Address for communication (6) Email address and Telephone No. with code (7) Qualification (8) National fellowship like ICAR/CSIR/UGC etc. if any (9) Whether SC/ST/OBC (10) Details of experience (Attested copies of degree certificate, proof of age, mark sheets). Original certificates should be produced for verification.</p>

<p>No TA/DA will be admissible to the candidates attending the test. The selected candidate will have to join immediately.</p>

<p>Advertisement: http://www.ctcri.org/careers/mithra_SRF.doc</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4107/natasa-przulj-lab</guid>
  <pubDate>Fri, 30 Aug 2013 06:29:17 -0500</pubDate>
  <link></link>
  <title><![CDATA[Nataša Pržulj Lab]]></title>
  <description><![CDATA[
<p>Nataša Pržulj Lab's research involves applications of graph theory, mathematical modeling, and computational techniques to solving large-scale problems in computational and systems biology.They are interested in computational and theoretical solutions to practical problems in many areas of systems biology, planar cell polarity, proteomics, cancer informatics, and drug discovery and design.</p>

<p>More at http://www.doc.ic.ac.uk/~natasha/index.html</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24984/ra-bioinformatics-at-nii</guid>
  <pubDate>Thu, 22 Oct 2015 01:56:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at NII]]></title>
  <description><![CDATA[
<p>NATIONAL INSTITUTE OF IMMUNOLOGY</p>

<p>NEW DELHI-110067</p>

<p>Applications are invited for the position of Research Associate (RA) for the following time-bound sponsored project as per the details given below:</p>

<p>1. BTIS project entitled, “National Infrastructural Facility in the Area of Immunology” funded by DBT</p>

<p>Research Associate (One Position only)</p>

<p>Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in</p>

<p>Educational Qualifications: Ph.D in Bioinformatics or Biological Sciences or Biotechnology with research experience and publication record in indexed peer reviewed journals in the area of bioinformatics or computational biology.</p>

<p>Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications &amp; experience Research Associate: Rs. 36,000/- per month plus 30% HRA</p>

<p>Job description &amp; Desired Knowledge: The candidate should be well versed in Programming in PERL/C++, HTML, CGI, web sever and portal development, computational analysis of protein structure &amp; function, molecular dynamics simulations and use of high performance computing systems.</p>

<p>General Terms &amp; Conditions:-</p>

<p>1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.</p>

<p>2. No hostel/ housing facility will be provided.</p>

<p>3. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.</p>

<p>4. No TA/DA will be paid for attending the interview, if called for.</p>

<p>5. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise and list of publications. 6. Canvassing in any form will be a disqualification.</p>

<p>HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., Email ID, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC/ST/PH and Women candidates are exempted from payment of fees) subject to submission of documentary proof), at the time of interview. (E-MAIL APPLICATIONS SHOULD MENTION BTIS-RA 2015 IN THE SUBJECT LINE)</p>

<p>LAST DATE OF RECEIPT OF APPLICATIONS: 29th October, 2015</p>

<p>Advertisement:</p>

<p>www1.nii.res.in/sites/default/files/projectappointments-Dr.Mohanty-29oct2015.pdf</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5255/walk-in-interview-indian-agricultural-statistics-research-institute</guid>
  <pubDate>Wed, 02 Oct 2013 15:40:17 -0500</pubDate>
  <link></link>
  <title><![CDATA[Walk-in-Interview @ Indian Agricultural Statistics Research Institute]]></title>
  <description><![CDATA[
<p>Indian Agricultural Statistics Research Institute<br />Library Avenue, Pusa, New Delhi – 110012</p>

<p>Walk-in-Interview</p>

<p>Walk-in-interview will be held on October 5, 2013 at 10:00 A.M. at IASRI, New Delhi for a project “A New Distributed Computing Framework for Data Mining” funded by Department of Electronics and Information Technology, Government of India for the following posts. The appointment will be on contractual basis upto 14th October, 2015 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.</p>

<p>Research Associate</p>

<p>    Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or</p>

<p>    Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 1st Division and at least two years of research experience</p>

<p>     Knowledge of Statistical Analysis /Bioinformatics tools for computational genomics.</p>

<p>     Knowledge of R/Perl programming language</p>

<p>Research Associate</p>

<p>    Ph.D. in Computer Science/ Computer Application / Bioinformatics/ Agricultural<br />    Statistics/ Statistics or equivalent or</p>

<p>    Post-Graduation in Computer Science/ Computer Application /Bioinformatics/ Agricultural Statistics/ Statistics or equivalent with 1st Division and at least two years of research experience</p>

<p>     Expertise in Java programming.<br />     Knowledge of system administration and networking under Linux environment.<br />     Knowledge of parallel programming and cluster computing.</p>

<p>Emoluments for Research Associate: Consolidated Rs:24000/- per month + HRA (for Ph.D. Degree holders) and Rs:23000/- per month + HRA (for Master’s Degree holders)</p>

<p>Age Limit: Age should be not more than 40 years (5 years relaxation for  SC/ST/women candidates and 3 years for OBC candidates as on date of interview).</p>

<p>Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph.</p>

<p>Original certificates/ Degrees are needed to be produced at the time of interview.</p>

<p>No T.A. /D.A. will be paid for appearing in the interview.</p>

<p>Advertisement: http://www.iasri.res.in/employment/employment.htm</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/1897/genetic-test-in-india</guid>
	<pubDate>Sun, 11 Aug 2013 10:54:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/1897/genetic-test-in-india</link>
	<title><![CDATA[Genetic Test in India]]></title>
	<description><![CDATA[<p>1.<strong>Xcode Life Sciences Pvt. Ltd.</strong><br /><span>6B, Eldorado,&nbsp;</span><br /><span>112, Nungambakkam High Road,</span><br /><span>Nungambakkam, Chennai 600034</span><br /><span>Tamil Nadu, India&nbsp;</span></p><p>2.<span><strong>Mapmygenome&trade;</strong><br /></span><span>Royal Demeure,HUDA Techno Enclave,<br />Plot No. 12/2, Sector-1 500 081&nbsp;<br />Madhapur,Hyderabad<br />AP, India</span></p><p>3.<strong>&nbsp;DNA Labs India</strong></p><p><strong><a href="http://www.dnalabsindia.com/lab.php">http://www.dnalabsindia.com/lab.php</a></strong></p><p>&nbsp;</p><p>4.<strong>MedGenome Labs Pvt Ltd</strong><br /><span>(Division of SciGenom Labs Pvt Ltd.)</span><br /><span>Plot no: 43A,SDF, 3rd floor</span><br /><span>A Block,CSEZ, Kakanad, Cochin</span><br /><span>Kerala - 682037&nbsp;</span><br /><span>Phone: 0484 - 2413399</span><br /><span>Fax: 0484 - 2413398</span><br /><span>Email:&nbsp;</span><a href="mailto:info@medgenome.com">info@medgenome.com</a></p><p>5.<strong>Narayana Nethralaya</strong></p><p><span>Narayana Hrudayalaya Campus</span><br /><span>Narayana Health City</span><br /><span># 258/A, Bommasandra, Hosur Road,&nbsp;</span><br /><span>Bangalore - 560 099 - INDIA.</span><br /><span>TEL: +91-80-66660655-0658&nbsp;</span><br /><span>FAX: +91-80-66660650&nbsp;</span><br /><span>Mobile: 9902 821128 (Emergency Only)</span><br /><span>e-mail:&nbsp;</span><a href="mailto:info@narayananethralaya.com">info@narayananethralaya.com</a></p><p>6.<strong>BioAxis DNA Research Centre Private Limited</strong><br />13-51,Sri Lakshmi Nagar colony,<br />Besides Big Bazar, Near Kamineni Hospitals<br />GSI Post BandalGuda (L B Nagar) Hydeabad-500068<br />Andhra Pradesh (<strong>India</strong>).<br />Phone :&nbsp;+91-40-24034503/+91-9246338983</p><p>7.<strong>Gene Guiide</strong></p><p>8th Floor, Embassy Towers, 7 Bungalows Rd, Versova, Andheri West, Mumbai-61&nbsp;<br />&nbsp;09167 117799&nbsp;<br />&nbsp;<a href="mailto:info@geneguiide.com" target="_blank">info@geneguiide.com</a>&nbsp;</p><p>See more at: http://www.geneguiide.com</p><p>8.<strong>INDIAN BIOSCIENCES</strong><br />Regd. Office:<br />G-2 (Ground Floor Rear), Kailash Colony, New Delhi - 110048, India.<br />Phone: +91 (0)11 29236088, Email: info@inbdna.com.</p><p>9.<strong>SRL Limited</strong></p><p>GP-26, MARUTI INDUSTRIAL ESTATE,</p><p>UDYOG VIHAR,SECTOR-18,</p><p>GURGAON - 122015</p><p>Tel: 0124-3001243 / 0124-3001209</p><p><strong>SRL Limited</strong><br />VASANT VIHAR, 8, PALAM MARG,<br />NEW DELHI - 110057<br />Tel: 011 - 4229 5333&nbsp;</p><p><strong>Website:</strong>&nbsp;<a href="http://www.srlworld.com/" target="_blank">http://www.srlworld.com</a><br /><strong>National Customer care number:</strong><br />Call Toll Free : 1800-222-660/1800-102-8282&nbsp;<br /><strong>E-mail id:</strong>&nbsp;<a href="mailto:customercare@srl.in">customercare@srl.in</a></p><p>10.<strong>Tata Memorial Centre</strong>,</p><p>Advanced Centre for Treatment, Research and Education in Cancer</p><p>Kharghar, Navi Mumbai - 410 210, INDIA.</p><p>Tel: +91-22-2740 5000</p><p>Fax: +91-22-2740 5085</p><p>E-mail: mail@actrec.gov.in</p><p style="text-align: center;">&nbsp;</p><p style="text-align: center;"><span style="font-size: large;"><a href="mailto:office@actrec.gov.in"></a></span></p><p>&nbsp;</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</guid>
	<pubDate>Fri, 27 Sep 2013 04:24:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</link>
	<title><![CDATA[Molecular Genetics Lecture]]></title>
	<description><![CDATA[<p><span>"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."&nbsp;</span></p>
<p><span>"<span><strong>Robert Sapolsky</strong> is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia</span></span></p><p>Address of the bookmark: <a href="http://www.youtube.com/watch?v=_dRXA1_e30o" rel="nofollow">http://www.youtube.com/watch?v=_dRXA1_e30o</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42804/one-year-position-for-a-bioinformatician-computational-biologist-in-population-genetics</guid>
  <pubDate>Fri, 05 Feb 2021 11:19:02 -0600</pubDate>
  <link></link>
  <title><![CDATA[One-year position for a bioinformatician / computational biologist in population genetics]]></title>
  <description><![CDATA[
<p>The successful candidate will work as support staff mainly in the development, application and maintenance of pipelines for handling large omics datasets (including whole-genome sequences, high-density genotypes and mRNA sequences). These pipelines cover pre-processing of data, statistical analyses and genome bioinformatics. The postholder will also provide support in producing high-level graphic representations of<br />these data and of results from their analysis.  Our team is part of UMR<br />7268 ADES research unit (Anthropologie bio-culturelle, Droit, Ethique<br />et Sant=E9), located at the Timone Faculty of Medicine (Aix-Marseille<br />University, 13005 Marseille). </p>

<p>JOB QUALIFICATION<br />- PhD/Engineer/MSc in bioinformatics, biostatistics, genetics/genomics<br />  or any related field.<br />- Advanced knowledge of Bash/Perl scripting and job management on a Unix<br />  HPC and in at least one basic language for data<br />  manipulation/statistics (such as R/Python/Matlab) are required.<br />- Knowledge of at least one programming language (e.g. C), experience<br />  processing -omics data or skills in advanced graphical representation<br />  of data would be a plus.</p>

<p>DURATION<br />1 year, not extensible</p>

<p>SALARY<br />Gross salary is commensurate with experience and grade (MSc from<br />1,882=80/month and PhD/equivalent from 2,099=80/month).</p>

<p>APPLICATIONS/OPENING<br />Please send a motivation letter, a CV and the names of two referees to<br />pierre.faux@univ-amu.fr. The expected starting date is April 1st, 2021;<br />the job offer will however remain opened until the position is filled.</p>

<p>Pierre Faux</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41222/best-practices-for-variant-calling-with-the-gatk</guid>
	<pubDate>Sat, 22 Feb 2020 03:07:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41222/best-practices-for-variant-calling-with-the-gatk</link>
	<title><![CDATA[Best Practices for Variant Calling with the GATK]]></title>
	<description><![CDATA[<p>The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad&rsquo;s Genome Analysis Toolkit (GATK) was version 3.3.</p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<ul>
<li><a href="https://software.broadinstitute.org/gatk/">Genome Analysis Toolkit</a></li>
</ul>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<table>
<tbody style="vertical-align: top;">
<tr>
<td>03/19/15</td>
<td>Introduction to High-Throughput Sequencing data formats and methods</td>
<td>Joel Thibault</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeY3g1M1ZjVjFrZ2s/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6696">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Introduction to the GATK</td>
<td>Geraldine Van der Auwera</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeVEJ1Z1pXUF9Ib3M/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6707">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Mapping, processing, and duplicate marking with Picard tools</td>
<td>Matt Sooknah</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeaGVrbE1GVV9SQkE/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6706">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Mapping and processing RNAseq</td>
<td>Ami Levy-Moonshine</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeLUkwUm5vTGl4bG8/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6705">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Indel realignment</td>
<td>Mark Fleharty</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeLTFzNndsNDBuVms/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6704">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Base quality score recalibration</td>
<td>David Roazen</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeZk1rMXpTYmZzTXc/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6703">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Introduction to variant discovery: calling cohorts</td>
<td>Louis Bergelson</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeQUFYUFRmM1hhRUE/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6702">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Variant calling and joint genotyping</td>
<td>Sheila Chandran</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeYzVTUGs0bjM3M1E/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6701">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Variant quality score recalibration</td>
<td>Bertrand Haas</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeSEpwRkNVQm4wdkE/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6700">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Introduction to working with variants</td>
<td>Yossi Farjoun</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWec0NqUTN2WTRuWWs/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6699">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Genotype refinement</td>
<td>Laura Gauthier</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeMzFldVF5SUp4dWM/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6698">Video</a></td>
</tr>
<tr>
<td>03/19/15</td>
<td>Annotation and variant evaluation</td>
<td>David Benjamin</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeWi1YMm42bWdpRE0/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6697">Video</a></td>
</tr>
</tbody>
</table><p>Address of the bookmark: <a href="https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1" rel="nofollow">https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1</a></p>]]></description>
	<dc:creator>biogeek</dc:creator>
</item>

</channel>
</rss>